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    GATD3 glutamine amidotransferase class 1 domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 8209, updated on 3-Nov-2024

    Summary

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    Official Symbol
    GATD3provided by HGNC
    Official Full Name
    glutamine amidotransferase class 1 domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:1273
    See related
    Ensembl:ENSG00000160221 MIM:601659; AllianceGenome:HGNC:1273
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ES1; HES1; KNPH; KNPI; GT335; GATD3A; C21orf33
    Summary
    This gene encodes a potential mitochondrial protein that is a member of the DJ-1/PfpI gene family. This protein is overexpressed in fetal Down syndrome brain. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
    Expression
    Ubiquitous expression in kidney (RPKM 72.1), heart (RPKM 46.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GATD3 in Genome Data Viewer
    Location:
    21q22.3
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (44133683..44145711)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (42486669..42501326)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (45553565..45565593)

    Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene trafficking protein particle complex subunit 10 Neighboring gene H2A.Z histone pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45487136-45487678 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45526826-45527342 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45530994-45531196 Neighboring gene Sharpr-MPRA regulatory region 9823 Neighboring gene PWP2 small subunit processome component Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:45553065-45553592 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:45553593-45554120 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:45554121-45554648 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13210 Neighboring gene ReSE screen-validated silencer GRCh37_chr21:45561103-45561261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:45566085-45566744 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18265 Neighboring gene uncharacterized LOC124905035 Neighboring gene long intergenic non-protein coding RNA 1678

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Cleavage-site motifs in mitochondrial targeting peptides. Gavel Y, et al. Protein Eng, 1990 Oct. PMID 2290832
    2. Proteomics of bovine mitochondrial RNA-binding proteins: HES1/KNP-I is a new mitochondrial resident protein. Ponamarev MV, et al. J Proteome Res, 2005 Jan-Feb. PMID 15707356
    3. Isolation of a human gene (HES1) with homology to an Escherichia coli and a zebrafish protein that maps to chromosome 21q22.3. Scott HS, et al. Hum Genet, 1997 May. PMID 9150728
    4. Localization of 16 exons to a 450-kb region involved in the autoimmune polyglandular disease type I (APECED) on human chromosome 21q22.3. Kudoh J, et al. DNA Res, 1997 Feb 28. PMID 9179495
    5. Isolation of cDNA for a novel human protein KNP-I that is homologous to the E. coli SCRP-27A protein from the autoimmune polyglandular disease type I (APECED) region of chromosome 21q22.3. Nagamine K, et al. Biochem Biophys Res Commun, 1996 Aug 14. PMID 8753807

    See all (55) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    2. ES1 protein expression was two-fold elevated (P < 0.01) in fetal Down syndrome brain compared to controls and may be a candidate protein involved in the pathogenesis of the brain deficit in DS.
      Title: Expression of cystathionine beta-synthase, pyridoxal kinase, and ES1 protein homolog (mitochondrial precursor) in fetal Down syndrome brain.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Anophthalmia-microphthalmia syndrome
    MedGen: C5680330 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial
    Names
    ES1 protein homolog, mitochondrial
    Keio novel protein I
    glutamine amidotransferase class 1 domain containing 3A
    glutamine amidotransferase like class 1 domain containing 3A
    glutamine amidotransferase-like class 1 domain-containing protein 3A, mitochondrial
    human HES1 protein, homolog to E.coli and zebrafish ES1 protein
    testis secretory sperm-binding protein Li 237E

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_021281.3 RefSeqGene

      Range
      5071..17099
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001320383.2 → NP_001307312.1  glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial isoform 3 precursor

      Status: REVIEWED

      Source sequence(s)
      BP283346, BQ011869, BQ647697
      UniProtKB/TrEMBL
      A0A096LP12, H7BYH1
      Related
      ENSP00000374340.3, ENST00000389690.7
      Conserved Domains (2) summary
      COG0693
      Location:51 → 173
      ThiJ; Putative intracellular protease/amidase [General function prediction only]
      cl00020
      Location:45 → 174
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    2. NM_001320384.2 → NP_001307313.1  glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AW292582, BI196781, BP283346, BQ011869
      Consensus CDS
      CCDS82680.1
      UniProtKB/TrEMBL
      F2Z2Q0
      Related
      ENSP00000396655.2, ENST00000427803.6
      Conserved Domains (2) summary
      COG0693
      Location:51 → 183
      ThiJ; Putative intracellular protease/amidase [General function prediction only]
      cl00020
      Location:45 → 174
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    3. NM_004649.8 → NP_004640.4  glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial isoform 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AB001517, AP001055
      Consensus CDS
      CCDS33580.1
      UniProtKB/Swiss-Prot
      A6NFJ6, A6NJY7, O00650, O00660, O15011, O15012, P0DPI2, P30042, P55346, P78474, Q92505, Q92507
      UniProtKB/TrEMBL
      A0A140VKB0
      Related
      ENSP00000291577.6, ENST00000291577.11
      Conserved Domains (1) summary
      cd03133
      Location:45 → 266
      GATase1_ES1; Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1

    4. NM_198155.5 → NP_937798.4  glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial isoform 2 precursor

      Status: REVIEWED

      Source sequence(s)
      AB001517, AP001055
      Consensus CDS
      CCDS33581.1
      UniProtKB/Swiss-Prot
      P30042
      Related
      ENSP00000344901.5, ENST00000348499.9
      Conserved Domains (1) summary
      cl00020
      Location:45 → 235
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    RNA

    1. NR_135220.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AB001517, AP001055

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000021.9 Reference GRCh38.p14 Primary Assembly

      Range
      44133683..44145711
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017028479.2 → XP_016883968.1  glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial isoform X1

      UniProtKB/TrEMBL
      H7C2G3
      Related
      ENSP00000405713.1, ENST00000419699.1
      Conserved Domains (1) summary
      cl00020
      Location:1 → 180
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060945.1 Alternate T2T-CHM13v2.0

      Range
      42486669..42501326
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324879.1 → XP_054180854.1  glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial isoform X2

    2. XM_054324877.1 → XP_054180852.1  glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial isoform X1

    3. XM_054324878.1 → XP_054180853.1  glutamine amidotransferase-like class 1 domain-containing protein 3, mitochondrial isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0DPI2.1 GenPept UniProtKB/Swiss-Prot:P0DPI2

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